SUMMARY: Olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important species of the Mediterranean region and one of the most ancient species domesticated. The availability of whole genome assemblies and annotations of olive tree cultivars and oleaster (O. europaea subsp. europaea var. sylvestris) has contributed to a better understanding of genetic and genomic differences between olive tree cultivars. However, compared to other plant species there is still a lack of genomic resources for olive tree populations that span the entire Mediterranean region. In the present study we developed the most complete genomic variation map and the most comprehensive catalog/resource of molecular variation to date for 89 olive tree genotypes originating from the entire Mediterranean basin, revealing the genetic diversity of this commercially significant crop tree and explaining the divergence/similarity among different variants. Additionally, the monumental ancient tree ‘Throuba Naxos’ was studied to characterize the potential origin or routes of olive tree domestication. Several candidate genes known to be associated with key agronomic traits, including olive oil quality and fruit yield, were uncovered by a selective sweep scan to be under selection pressure on all olive tree chromosomes. To further exploit the genomic and phenotypic resources obtained from the current work, genome‐wide association analyses were performed for 23 morphological and two agronomic traits. Significant associations were detected for eight traits that provide valuable candidates for fruit tree breeding and for deeper understanding of olive tree biology.

Plant responses to salinity are becoming increasingly understood, however, salt priming mechanisms remain unclear, especially in perennial fruit trees. Herein, we showed that low-salt pre-exposure primes olive (Olea europaea) plants against high salinity stress. We then performed a proteogenomic study to characterize priming responses in olive roots and leaves. Integration of transcriptomic and proteomic data along with metabolic data revealed robust salinity changes that exhibit distinct or overlapping patterns in olive tissues, among which we focused on sugar regulation. Using the multi-crossed -omics data set, we showed that major differences between primed and nonprimed tissues are mainly associated with hormone signaling and defense-related interactions. We identified multiple genes and proteins, including known and putative regulators, that reported significant proteomic and transcriptomic changes between primed and nonprimed plants. Evidence also supported the notion that protein post-translational modifications, notably phosphorylations, carbonylations and S-nitrosylations, promote salt priming. The proteome and transcriptome abundance atlas uncovered alterations between mRNA and protein quantities within tissues and salinity conditions. Proteogenomic-driven causal model discovery also unveiled key interaction networks involved in salt priming. Data generated in this study are important resources for understanding salt priming in olive tree and facilitating proteogenomic research in plant physiology.

The term "terroir" has been widely employed to link differential geographic phenotypes with sensorial signatures of agricultural food products, influenced by agricultural practices, soil type, and climate. Nowadays, the geographical indications labeling has been developed to safeguard the quality of plant-derived food that is linked to a certain terroir and is generally considered as an indication of superior organoleptic properties. As the dynamics of agroecosystems are highly intricate, consisting of tangled networks of interactions between plants, microorganisms, and the surrounding environment, the recognition of the key molecular components of terroir fingerprinting remains a great challenge to protect both the origin and the safety of food commodities. Furthermore, the contribution of microbiome as a potential driver of the terroir signature has been underestimated. Herein, we present a first comprehensive view of the multi-omic landscape related to transcriptome, proteome, epigenome, and metagenome of the popular Protected Geographical Indication potatoes of Naxos.

High‐depth whole‐genome resequencing of 53 diverse fig tree genotypes yielded a rich dataset of genetic variants. We successfully identified 5,501,460 single‐nucleotide polymorphisms (SNPs) and 1,228,537 insertions and deletions (InDels), providing a high‐density and excellent‐quality genetic map of the fig tree. We also performed a detailed population structure analysis, dividing the 53 genotypes into three geographical groups and assessing their genetic diversity and divergence. Analysis of structural variants (SVs) and copy number variations (CNVs) revealed their potential functional impact, particularly in plant‐pathogen interaction and secondary metabolism. Metabolomic fingerprinting of fig genotypes uncovered extensive variation in primary metabolites and polyphenolic compounds, highlighting the influence of genotype on fruit quality traits such as nutritional content and bioactive compound composition. The genome‐wide association study (GWAS) identified critical SNPs associated with fruit quality and morphological features. The discovery of significant candidate genes, such as AGL62, GDSL, and COBRA‐like protein 4 genes, offers promising targets for marker‐assisted selection and genome editing approaches to improve fig fruit morphological and quality traits. This extensive genomic analysis of fig trees enhances our understanding of the genetic basis of important agronomic traits and provides a rich resource for future research in this economically and nutritionally significant fruit.

Ultraviolet-C (UV-C) irradiation delays fruit ripening, yet the underlying mechanisms remain unclear. We investigated tissue-specific responses of peach fruit (Prunus persica L. Batsch) to UV-C by analyzing the peel and flesh separately. UV-C treatment altered central metabolism, promoted anthocyanin accumulation and coloration, and delayed ripening, as evidenced by reduced fruit softening and water loss. However, UV-C enhanced ethylene production and upregulated ethylene-related genes, indicating a reconfiguration of the ethylene response. Among UV-C-responsive genes, the APETALA2/Ethylene Response Factor (AP2/ERF) transcription factor family was most affected, with Ethylene Response Factor 1A (ERF1A) showing the strongest induction in the treated peel, suggesting its role as a key integrator of the UV-C-induced ripening delay. UV-C increased the levels of DNA 5-methylcytosine and RNA N6-methyladenosine in the peel, without altering cytosine methylation or causing mutations in ERF1A. Silencing ERF1A via RNA interference confirmed that it regulates ethylene production, softening, and ripening-associated metabolites. Immunolocalization revealed changes in the cell wall components of ERF1A-silenced fruit, including arabinogalactan, pectin, and xyloglucan. ERF1A-silenced peels exhibited elevated auxin and salicylic acid levels and reduced abscisic acid content. Additionally, ERF1A suppression altered the biosynthesis of sugars, phenolic compounds, and volatiles. We found extensive proteome reprogramming in ERF1A-silenced peels and identified putative ERF1A target genes that either contain ERF1A-binding sites or are associated with firmness, ethylene signaling, phytohormone metabolism, and color. Notably, Carboxylesterase 11 (PpCXE11), Carboxylesterase 13 (PpCXE13), and Salicylic acid-binding protein 2 (PpSABP2) emerged as potential ERF1A targets. These findings identify ERF1A as a central regulator mediating UV-C-induced ripening delay through modulation of ethylene signaling and downstream ripening pathways.

Abiotic stress, particularly heat and drought, significantly impacts plant reproductive development, threatening crop productivity and food security. Understanding stress tolerance mechanisms requires a multi‐level approach that integrates physiological, biochemical, and molecular traits in different experimental settings. This review explores key methodologies for assessing resilience to single and combined abiotic stress in reproductive tissues, from growth chamber experiments to greenhouse and field trials. Essential physiological and biochemical traits indicative of stress responses are highlighted alongside molecular pathways that provide deeper insights into adaptation to drought and heat stress. The use of multi‐omics techniques, including transcriptomics, proteomics, and metabolomics, as powerful tools for identifying novel stress‐associated traits is discussed, with an emphasis on the integration of these techniques into a holistic framework, which also incorporates single‐cell approaches. Finally, we address the limitations of the current methodologies and propose future research directions to improve stress resilience assessment in plant reproductive development.